A label-free assay of exonuclease activity using a pyrosequencing technique

Systematic Probing of the Sequence Selectivity of Exonuclease III with a Photosensitization Colorimetric Assay

Exonuclease III (Exo III) is an important enzymatic tool that is being widely used in molecular biology, biotechnology, and bioassay development. Exo III prefers to cleave double-stranded DNA (dsDNA) with blunt and recessed 3'-termini rather than their protruding counterpart. While it has been accepted that a short 3'-overhang (e.g., >4 nt) is necessary to protect a dsDNA from Exo III cleavage, critical roles of the length and sequence of this 3'-overhang remain unexplored. Herein, we develop a novel light-induced colorimetric assay allowing the systematic probe of the sequence selectivity of Exo III in a rapid and high-throughput manner. Our finding that Exo III is highly specific to 3'-overhang in terms of both length and sequence will be valuable for guiding the design of bioassays and DNA manipulating tools mediated by Exo III.

A triple-color fluorescent probe for multiple nuclease assays

We develop a triple-color fluorescent probe which may function as a lab-on-a-DNA-molecule for simultaneous detection of multiple nucleases.

Effects of cations on small fragment of DNA polymerase I using a novel FRET assay

DNA polymerase I (PolI) digested by protease produces a small fragment (SF) containing 5'-3' exonuclease activity. The 5'-3' exonuclease activity of polI cleaves the downstream RNA primer strands during DNA replication in vivo. Previous in vitro studies suggested its capability of cleaving duplex from 5' terminal and a flap-structure-specific endonuclease activity. From the crystal structures of other nucleases and biochemical data, a two-metal-ion mechanism has been proposed but has not been determined. In this study, we cloned, expressed, and purified the SF protein, and established a novel fluorescence resonance energy transfer (FRET) assay to analyze the catalytic activity of the SF protein. The effects of several metal ions on its catalytic capability were analyzed using this FRET assay. Results showed that Mg2+, Mn2+, and Zn2+ were able to activate the cleavage of SF, while Ca2+, Ni2 +, and Co2+ were not suitable for SF catalysis. The effects of K+, Na+, and dNTP were also determined.

Ultrasensitive detection of 3′-5′ exonuclease enzymatic activity using molecular beacons

An ultrasensitive and rapid fluorescence assay was developed for the detection of 3′-5′ exonuclease activity using molecular beacons.

In situ, real-time monitoring of the 3' to 5' exonucleases secreted by living cells

Enzymes containing 3'-5' exonuclease activities play vital roles in maintaining genome stability. Though a wide variety of methods have been developed for detection of these enzymes, few of them can be directly applied for in situ and real-time monitoring of the secretion of these active substances by living cells. Taking advantages of the free 3'-end of stacked guanine-quenched photoinduced electron transfer fluorescent probes, here we demonstrate a novel assay capable of in situ and real-time monitoring of the 3'-5' exonucleases secreted by living cells. The detection limit of the new method achieved as low as 0.04 U/mL, allowing direct monitoring of the target enzymes in an extracellular environment without preconcentration steps. False positive signals caused by other nonspecific enzymes were easily ruled out by the use of a control probe with the 3'-end modified with exonuclease-resistant phosphorothioate guanines. Using Alexa Fluor 488 as the fluorophore, the probe is adaptable to a wide range of pH conditions. The approach was successfully applied for in situ, real-time monitoring of the 3'-5' exonucleases secreted by suspension cells of Arabidopsis thaliana. It also holds great potential for in situ and real-time detection of many other DNA end-processing enzymes produced by other types of cells.